COMSATS University Islamabad-
Abbottabad Campus
Course: Research Methods And Scientific Writing (Bty466)
Assignment Title: Classify the research article based on the types of
research
ASSIGNMENT NO: 01
Submitted by:
Adil Hayat (Fa21-BTY-008)
Syed Faizan Shah (Fa21-BTY-024)
Submitted To: Dr. Yasar Sajjad
Date Of Submission: April 15, 2025
Article 1
Title: Natural transformation allows transfer of SCCmec-mediated methicillin
resistance in Staphylococcus aureus biofilms
1. Application Perspective: Applied Research
• Reasoning: This research investigates the mechanism behind the transfer of antibiotic
resistance genes (SCCmec) within S. aureus biofilms, with implications for public health
and antibiotic resistance control strategies. The findings have direct utility in healthcare
and microbial genetics.
2. Objective Perspective: Explanatory + Descriptive
• Reasoning:
o Explanatory: Explains how natural transformation contributes to horizontal gene
transfer (HGT), particularly SCCmec elements.
o Descriptive: Describes gene expression changes, biofilm conditions,
transformation efficiency, and observed outcomes of SCCmec transfer.
3. Enquiry Mode Perspective: Mixed Methods Research
• Reasoning: The study includes both quantitative gene expression levels, transformation
frequency data, biofilm biomass, and qualitative observations about genetic interactions
and mechanisms.
Article 2
Title: Tyrosol blocks E. coli anaerobic biofilm formation via YbfA and FNR to
increase antibiotic susceptibility
1. Application Perspective: Applied Research
• Reasoning: The study investigates how naturally occuring compound tyrosol inhibits
anaerobic biofilm formation and enhances antibiotic susceptibility for E. coli and P.
aeruginosa. This has direct implications for treatment strategies against biofilm associated
infections.
2. Objective Perspective: Explanatory + Correlational
• Reasoning:
o Explanatory: Molecular mechanism; YbfA blocks by tyrosol; FNR and NO levels
reduced, causing lower biofilm formation is explained.
o Correlational: It shows associations among variables like tyrosol concentration,
YbfA/FNR expression, NO production and biofilm formation.
3. Enquiry Mode Perspective: Mixed Methods Research
• Reasoning: Combines quantitative measurements (e.g., NO levels, gene expression,
antibiotic susceptibility assays) with qualitative insights into regulatory pathways and
functional protein interactions.
Article 3
Title: Legacies of temperature fluctuations promote stability in marine biofilm
communities
1. Application Perspective: Pure Research
• Reasoning: This study aims to understand how historical temperature fluctuation regimes
affect the stability of marine biofilm communities. It builds ecological theory around
environmental legacy effects and microbial functional redundancy without aiming at an
immediate practical solution.
2. Objective Perspective: Descriptive + Explanatory
• Reasoning:
o Descriptive: Describes community dynamics in marine biofilms exposed to
fluctuating vs. constant temperature regimes.
o Explanatory: Explains how different warming regimes affect functional
redundancy and stability dimensions (resistance, resilience, recovery rate).
3. Enquiry Mode Perspective: Mixed Methods Research
• Reasoning: The study uses quantitative metrics (e.g., recovery rate, biomass, diversity
indices) and qualitative trait-based assessments (e.g., stress tolerance vs. growth trade-offs,
trait categorization) to evaluate ecological responses.
Article 4
Title: Biogel scavenging slows the sinking of organic particles to the ocean depths
1. Application Perspective: Pure Research
• Reasoning: This study explores the fundamental biophysical mechanisms—specifically
biogel scavenging—that affect the sinking velocity of organic marine particles. Its primary
goal is to advance scientific understanding of oceanic carbon fluxes, not an immediate
applied outcome.
2. Objective Perspective: Explanatory
• Reasoning: The study explains why and how biogels reduce the sinking speed of marine
particles by integrating fluid dynamics, particle biology, and biogeochemistry into a
cohesive mechanistic model. It tests cause-effect relationships using a controlled
millifluidic experiment and a theoretical model.
3. Enquiry Mode Perspective: Mixed Methods Research
• Reasoning: Combines:
o Quantitative: Sinking speed measurements, biogel layer thickness, particle drag
coefficients, and model simulation outputs.
o Qualitative: Morphological changes due to biogel interaction, biofilm adhesion
traits, and microscopic visual interpretation (e.g., biogel tendril formation).
Article 5
Title: Bacteria use exogenous peptidoglycan as a danger signal to trigger biofilm
formation
1. Application Perspective: Pure Research
• Reasoning: This study focuses on uncovering a general bacterial signaling mechanism
using exogenous peptidoglycan as a universal "danger signal" that triggers biofilm
formation across species. The main intent is foundational discovery, not practical
deployment.
2. Objective Perspective: Exploratory + Explanatory
• Reasoning:
o Exploratory: Investigates a previously unknown mechanism—whether exogenous
peptidoglycan acts as a conserved danger signal.
o Explanatory: Explains how the signaling cascade results in three-dimensional
biofilm formation and provides protection against phage attack.
3. Enquiry Mode Perspective: Mixed Methods Research
• Reasoning:
o Quantitative: Uses biofilm volume measurements, phage titers, gene expression
levels, etc.
o Qualitative: Observations of 2D vs. 3D biofilm architecture, bacterial species
response types, and danger signal specificity.
Article 6
Title: On the effectiveness of electrical characterization of mature Staphylococcal
Biofilm
1. Application Perspective: Applied Research
• Reasoning: The study investigates how electrical fields interact with mature S. aureus
biofilms using impedance spectroscopy. It aims to evaluate diagnostic reliability and
uncover possible therapeutic effects of electric fields—both of which have practical
implications in medical diagnostics and treatment design.
2. Objective Perspective: Descriptive + Exploratory
• Reasoning:
o Descriptive: Measures impedance responses of biofilm under various conditions
(frequency, amplitude, exposure time).
o Exploratory: Uncovers unexpected destructive interactions and proposes novel
therapeutic implications from those observations.
3. Enquiry Mode Perspective: Mixed Methods Research
• Reasoning:
o Quantitative: Electrical impedance values, frequency ranges, biomass reduction
percentages, etc.
o Qualitative: Observations of biofilm structural integrity, microbial behavior post-
exposure, and device performance interpretation.
Article 7
Title: Biofilm proficient Bacillus subtilis prevents neurodegeneration in
Caenorhabditis elegans Parkinson’s disease models via PMK-1/p38 MAPK and
SKN-1/Nrf2 signaling
1. Application Perspective: Applied Research
• Reasoning: This study investigates the neuroprotective effects of B. subtilis biofilms in C.
elegans Parkinson’s disease (PD) models, linking bacterial biofilm presence to potential
therapeutic strategies. The intention is translational, contributing toward microbiome-
based therapeutics in neurodegeneration.
2. Objective Perspective: Explanatory + Correlational
• Reasoning:
o Explanatory: Explains how biofilm-forming B. subtilis activates PMK-1/SKN-1
signaling to protect dopaminergic neurons.
o Correlational: Shows relationships between biofilm presence, neuron survival,
alpha-synuclein aggregation, and behavioral outcomes.
3. Enquiry Mode Perspective: Mixed Methods Research
• Reasoning:
o Quantitative: Measures neurodegeneration levels, behavioral outputs, lifespan,
alpha-synuclein aggregation levels.
o Qualitative: Observes gene expression profiles, stress responses, phenotypic
effects of bacterial colonization.
Article 8
Title: Virulence factors and biofilm forming ability of Staphylococcus species
isolated from skeletal lesions of broiler chickens
1. Application Perspective: Applied Research
• Reasoning: The research directly addresses the practical issue of skeletal infections in
poultry caused by biofilm-forming Staphylococcus species. It provides insights for disease
control strategies, improving animal welfare and production performance in commercial
poultry farming.
2. Objective Perspective: Descriptive + Correlational
• Reasoning:
o Descriptive: Catalogs prevalence, anatomical distribution, and species
identification of Staphylococcus isolates.
o Correlational: Analyzes associations between biofilm-forming capacity, virulence
factor expression (e.g., DNase, gelatinase), and lesion type.
3. Enquiry Mode Perspective: Mixed Methods Research
• Reasoning:
o Quantitative: Measures biofilm density, enzymatic activity, prevalence rates,
lesion incidence, gene expression frequency.
o Qualitative: Identifies species, lesion descriptions, adhesin gene presence (e.g.,
eno), and infection profiles.
Article 9
Title: Synthetic phosphoethanolamine-modified oligosaccharides reveal the
importance of glycan length and substitution in biofilm-inspired assemblies
1. Application Perspective: Pure Research
• Reasoning: The study focuses on developing synthetic glycan structures and
understanding their physicochemical behavior in co-assemblies. It is foundational and
method-driven.
2. Objective Perspective: Explanatory + Descriptive
• Reasoning:
o Explanatory: Explains how glycan length and substitution affect
mechanical/structural properties.
o Descriptive: describes co-assembly behavior and matrix characteristics.
3. Enquiry Mode Perspective: Quantitative
• Reasoning: Entirely based on measurable outputs: stiffness, adhesion force (nN), beta-
sheet formation rate, fiber dimensions
Article 10
Title: Preliminary survey of biofilm forming, antibiotic resistant Escherichia coli
in fishes from land-based aquaculture systems and open water bodies in
Bangladesh
1. Application Perspective: Applied Research
• Reasoning: Addresses real-world public health concerns by identifying MDR E. coli and
biofilm formation in food sources, aimed at guiding monitoring and policy development.
2. Objective Perspective: Descriptive + Correlational
• Reasoning:
o Descriptive: Describes prevalence of E. coli, resistance genes, and biofilm
formation.
o Correlational: Correlates gene presence with resistance and fish types using
bivariate statistical analysis.
3. Enquiry Mode Perspective: Mixed Methods Research
• Reasoning:
o Quantitative: Quantitative data (percent resistance, gene frequency, OD570
values).
o Qualitative: Qualitative aspects (biofilm morphology, sampling source, fish
species behavior).
